Windows 98 uses preemptive multitasking for Win32-based applications. This means that the operating system takes control away from or gives control to another running task, depending on the needs of the system.

With Windows 3.1, applications ran concurrently through a method known as cooperative multitasking. Using this method, the operating system required an application to check the message queue periodically and to relinquish control of the system to other running applications. Applications that did not check the message queue would effectively "hog" CPU time and prevent the user from switching to another application. For compatibility reasons, Windows 98 cooperatively multitasks Win16-based applications.